Table 2.
Selected C. acetobutylicum ATCC 824 genes showing a significant response after exposure to 50 mM butanol compared to nonexposed controls by using a mixed-model analysisa
| Substrate | Product nameb | COG EHIPc | Locus tag | Differenced | −Log10P value |
|---|---|---|---|---|---|
| S | O-Acetylhomoserine sulfhydrylase | E | CAC0102 | 2.31573 | 13.35289 |
| S | Adenylylsulfate kinase | P | CAC0103 | 2.31299 | 10.6627 |
| S | ABC-type probable sulfate transporter, periplasmic binding protein | P | CAC0106 | 2.19078 | 9.92702 |
| S | ABC-type sulfate transporter, ATPase component | P | CAC0107 | 2.22341 | 4.68265 |
| S | ABC-type probable sulfate transporter, permease protein | P | CAC0108 | 1.63887 | 6.53352 |
| S | Sulfate adenylyltransferase subunit 2 | E | CAC0109 | 2.44843 | 10.70661 |
| S | GTPase, sulfate adenylate transferase subunit 1 | P | CAC0110 | 2.13862 | 7.30271 |
| Asp | Aspartate semialdehyde dehydrogenase | E | CAC0568 | 0.90651 | 5.24713 |
| Lys | Diaminopimelate decarboxylase LisA | E | CAC0608 | 0.94998 | 2.35148 |
| Fe | Ferrichrome transport permease | P | CAC0788 | 0.68284 | 4.07679 |
| Cys | γ-Cystathionine synthase | E | CAC0930 | 1.52732 | 7.36916 |
| His | ATP phosphoribosyltransferase catalytic subunit | E | CAC0936 | 1.28815 | 3.9961 |
| His | Histidinol dehydrogenase | E | CAC0937 | 1.63942 | 10.93148 |
| His | Imidazoleglycerol-phosphate dehydratase | E | CAC0938 | 1.30102 | 7.31492 |
| His | Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase | E | CAC0940 | 0.87342 | 6.57009 |
| His | Phosphoribosyl-AMP cyclohydrolase | E | CAC0942 | 0.57879 | 3.28315 |
| Arg | Argininosuccinate lyase | E | CAC0974 | 1.65485 | 10.71147 |
| 5-Formyltetrahydrofolate cycloligase | H | CAC1090 | 0.70186 | 2.19531 | |
| Asp | Aspartate kinase I | E | CAC1810 | 0.707 | 2.50719 |
| Mo | Molybdopterin biosynthesis enzyme, MoeA, fused to the molybdopterin-binding domain | P | CAC2020 | 0.92291 | 3.22569 |
| Cys | Cysteine synthase/cystathionine beta-synthase, CysK | E | CAC2235 | 0.40506 | 2.13166 |
| Arg/Lys | N-Acetylornithine aminotransferase | E | CAC2388 | 1.51803 | 7.14475 |
| Urea | Acetylglutamate kinase | E | CAC2389 | 1.07553 | 4.10307 |
| Urea | N-Acetyl-gamma-glutamyl-phosphate reductase | E | CAC2390 | 1.7949 | 7.75867 |
| Fe | Ferric uptake regulator (FUR family), YGAG B. subtilis ortholog | P | CAC2634 | 2.70695 | 4.15283 |
| 3-Hydroxybutyryl-CoA dehydrogenase | I | CAC2708 | 0.54094 | 2.51473 | |
| Lipid | Butyryl-CoA dehydrogenase | I | CAC2711 | 0.61838 | 3.75509 |
| 3-Hydroxybutyryl-CoA dehydratase | I | CAC2712 | 0.56573 | 3.00566 | |
| Lys | Lysine-specific permease | E | CAC3164 | 0.92611 | 5.19834 |
| Dihydroxy-acid dehydratase | E | CAC3170 | 0.55559 | 2.16606 | |
| Met | Homocysteine methyltransferase | E | CAC3348 | 0.4169 | 2.22381 |
| Lipid | 3-Oxoacyl-acyl carrier protein reductase | I | CAC3462 | 0.78625 | 5.23967 |
| Lipid | Phosphatidylglycerophosphate synthase | I | CAC3596 | 1.88139 | 5.43757 |
| K | K+-transporting ATPase, c chain | P | CAC3680 | 0.65812 | 3.02242 |
| K | Potassium-transporting ATPase subunit B | P | CAC3681 | 0.74665 | 3.01109 |
The mixed-model analysis (JMP Genomics [SAS, Cary, NC]) was performed on data obtained from microarray results (3) comparing the cells exposed to butanol for 360 min [e.g., differential of time × treatment = (360 min butanol) − (360 min control)]. Figure 2B shows the frequencies of genes displaying up- or downregulation after mixed-model analysis (14). Data were obtained from cells cultivated in clostridial growth medium (CGM [69]).
YGAG, synonym for the PerR protein, which encodes a FUR homolog in B. subtilis; CoA, coenzyme A.
COGs (clusters of orthologous groups) (www.ncbi.nlm.nih.gov/COG/grace/uni.html).
Difference in P values are shown.